PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: School health assessment tools: a systematic review of measurement in primary schools
items: Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage
items: Microbial and chemical dynamics of a toxic dinoflagellate bloom
items: Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam
items: Habitat preferences rather than morphological traits affect the recovery process of Collembola (Arthropoda, Hexapoda) on a bare saline–alkaline land
items: Quantifying uncertainty in annual runoff due to missing data
items: The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes
items: Ethyl pyruvate inhibits glioblastoma cells migration and invasion through modulation of NF-κB and ERK-mediated EMT
items: Prediction of human fetal–maternal blood concentration ratio of chemicals
items: The effects of “Fangcang, Huoshenshan, and Leishenshan” hospitals and environmental factors on the mortality of COVID-19

School health assessment tools: a systematic review of measurement in primary schools
type: item
type: AcademicArticle
description: Background This systematic review aimed to investigate the psychometric properties of the school health’s assessment tools in primary schools through COSMIN Risk of Bias checklist. We examined the studies that have addressed the measurement properties of school-health instruments to give a clear overview of the quality of all available tools measuring school health in primary schools. This systematic review was registered in PROPERO with the Registration ID: CRD42020158158. Method Databases of EBSCOhost, PubMed, ProQuest, Wily, PROSPERO, and OpenGrey were systematically searched without any time limitation to find all full-text English journal articles studied at least one of the COSMIN checklist measurement properties of a school-health assessment tool in primary schools. The instruments should be constructed based on a school health model. The eligible studies were assessed by COSMIN Risk of Bias checklist to report their quality of methodology for each measurement property and for the whole study by rating high, moderate or low quality. Results At the final screening just seven studies remained for review. Four studies were tool development, three of them were rated as “adequate” and the other study as “very good”; five studies examined the content validity, three of them were appraised as “very good”, and the two remaining as “inadequate”. All seven studies measured structural validity, three of them were evaluated as “very good”, three other were scored as “adequate”, and the last study as “inadequate”. All the seven studies investigated the internal consistency, five of them were assessed as “very good”, one was rated as “doubtful”, and the last one as “inadequate”. Just one study examined the cross-cultural validity and was rated as “adequate”. Finally, all seven studies measured reliability, two of them were rated as “very good” and the rest five studies were appraised as “doubtful”. All rating was based on COSMIN checklist criteria for quality of measuremen…
format: application/pdf
format: text/html
creator: Maryam Kazemitabar
creator: Ali Moghadamzadeh
creator: Mojtaba Habibi
creator: Rezvan Hakimzadeh
creator: Danilo Garcia
subject: Health Policy
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.9459
publisher: PeerJ Inc.
rights: © 2020 Kazemitabar et al.
abstract: Background This systematic review aimed to investigate the psychometric properties of the school health’s assessment tools in primary schools through COSMIN Risk of Bias checklist. We examined the studies that have addressed the measurement properties of school-health instruments to give a clear overview of the quality of all available tools measuring school health in primary schools. This systematic review was registered in PROPERO with the Registration ID: CRD42020158158. Method Databases of EBSCOhost, PubMed, ProQuest, Wily, PROSPERO, and OpenGrey were systematically searched without any time limitation to find all full-text English journal articles studied at least one of the COSMIN checklist measurement properties of a school-health assessment tool in primary schools. The instruments should be constructed based on a school health model. The eligible studies were assessed by COSMIN Risk of Bias checklist to report their quality of methodology for each measurement property and for the whole study by rating high, moderate or low quality. Results At the final screening just seven studies remained for review. Four studies were tool development, three of them were rated as “adequate” and the other study as “very good”; five studies examined the content validity, three of them were appraised as “very good”, and the two remaining as “inadequate”. All seven studies measured structural validity, three of them were evaluated as “very good”, three other were scored as “adequate”, and the last study as “inadequate”. All the seven studies investigated the internal consistency, five of them were assessed as “very good”, one was rated as “doubtful”, and the last one as “inadequate”. Just one study examined the cross-cultural validity and was rated as “adequate”. Finally, all seven studies measured reliability, two of them were rated as “very good” and the rest five studies were appraised as “doubtful”. All rating was based on COSMIN checklist criteria for quality of measuremen…
bibliographic citation: Kazemitabar et al. (2020) School health assessment tools: a systematic review of measurement in primary schools. PeerJ 8:e9459 https://doi.org/10.7717/peerj.9459
date submitted: 2020-02-05
date accepted: 2020-06-09
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kazemitabar
  given name: Maryam
author list: Agent
  family name: Moghadamzadeh
  given name: Ali
author list: Agent
  family name: Habibi
  given name: Mojtaba
author list: Agent
  family name: Hakimzadeh
  given name: Rezvan
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.9459
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: ©2020 Kazemitabar et al.
attribution name: Kazemitabar et al.

Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage
type: item
type: AcademicArticle
description: Background Bone marrow adipocyte (BMA), closely associated with bone degeneration, shares common progenitors with osteoblastic lineage. However, the intrinsic mechanism of cells fate commitment between BMA and osteogenic lineage remains unclear. Methods Gene Expression Omnibus (GEO) dataset GSE107789 publicly available was downloaded and analyzed. Differentially expressed genes (DEGs) were analyzed using GEO2R. Functional and pathway enrichment analyses of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were conducted by The Database for Annotation, Visualization and Integrated Discovery and Gene set enrichment analysis software. Protein–protein interactions (PPI) network was obtained using STRING database, visualized and clustered by Cytoscape software. Transcriptional levels of key genes were verified by real-time quantitative PCR in vitro in Bone marrow stromal cells (BMSCs) undergoing adipogenic differentiation at day 7 and in vivo in ovariectomized mice model. Results A total of 2,869 DEGs, including 1,357 up-regulated and 1,512 down-regulated ones, were screened out from transcriptional profile of human BMSCs undergoing adipogenic induction at day 7 vs. day 0. Functional and pathway enrichment analysis, combined with modules analysis of PPI network, highlighted ACSL1, sphingosine 1-phosphate receptors 3 (S1PR3), ZBTB16 and glypican 3 as key genes up-regulated at the early stage of BMSCs adipogenic differentiation. Furthermore, up-regulated mRNA expression levels of ACSL1, S1PR3 and ZBTB16 were confirmed both in vitro and in vivo. Conclusion ACSL1, S1PR3 and ZBTB16 may play crucial roles in early regulation of BMSCs adipogenic differentiation
format: application/pdf
format: text/html
creator: Pengyu Chen
creator: Mingrui Song
creator: Yutian Wang
creator: Songyun Deng
creator: Weisheng Hong
creator: Xianrong Zhang
creator: Bin Yu
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
subject: Orthopedics
description: doi:10.7717/peerj.9484
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background Bone marrow adipocyte (BMA), closely associated with bone degeneration, shares common progenitors with osteoblastic lineage. However, the intrinsic mechanism of cells fate commitment between BMA and osteogenic lineage remains unclear. Methods Gene Expression Omnibus (GEO) dataset GSE107789 publicly available was downloaded and analyzed. Differentially expressed genes (DEGs) were analyzed using GEO2R. Functional and pathway enrichment analyses of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were conducted by The Database for Annotation, Visualization and Integrated Discovery and Gene set enrichment analysis software. Protein–protein interactions (PPI) network was obtained using STRING database, visualized and clustered by Cytoscape software. Transcriptional levels of key genes were verified by real-time quantitative PCR in vitro in Bone marrow stromal cells (BMSCs) undergoing adipogenic differentiation at day 7 and in vivo in ovariectomized mice model. Results A total of 2,869 DEGs, including 1,357 up-regulated and 1,512 down-regulated ones, were screened out from transcriptional profile of human BMSCs undergoing adipogenic induction at day 7 vs. day 0. Functional and pathway enrichment analysis, combined with modules analysis of PPI network, highlighted ACSL1, sphingosine 1-phosphate receptors 3 (S1PR3), ZBTB16 and glypican 3 as key genes up-regulated at the early stage of BMSCs adipogenic differentiation. Furthermore, up-regulated mRNA expression levels of ACSL1, S1PR3 and ZBTB16 were confirmed both in vitro and in vivo. Conclusion ACSL1, S1PR3 and ZBTB16 may play crucial roles in early regulation of BMSCs adipogenic differentiation
bibliographic citation: Chen et al. (2020) Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage. PeerJ 8:e9484 https://doi.org/10.7717/peerj.9484
date submitted: 2020-03-20
date accepted: 2020-06-15
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Pengyu
author list: Agent
  family name: Song
  given name: Mingrui
author list: Agent
  family name: Wang
  given name: Yutian
author list: Agent
  family name: Deng
  given name: Songyun
author list: Agent
  family name: Hong
  given name: Weisheng
author list: Agent
  family name: Zhang
  given name: Xianrong
author list: Agent
  family name: Yu
  given name: Bin
doi: 10.7717/peerj.9484
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: © 2020 Chen et al.
attribution name: Chen et al.

Microbial and chemical dynamics of a toxic dinoflagellate bloom
type: item
type: AcademicArticle
description: Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.
format: application/pdf
format: text/html
creator: Nastassia V. Patin
creator: Emily Brown
creator: Gabriella Chebli
creator: Claire Garfield
creator: Julia Kubanek
creator: Frank J. Stewart
subject: Computational Biology
subject: Marine Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.9493
publisher: PeerJ Inc.
rights: © 2020 Patin et al.
abstract: Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.
bibliographic citation: Patin et al. (2020) Microbial and chemical dynamics of a toxic dinoflagellate bloom. PeerJ 8:e9493 https://doi.org/10.7717/peerj.9493
date submitted: 2020-03-27
date accepted: 2020-06-17
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Patin
  given name: Nastassia V.
author list: Agent
  family name: Brown
  given name: Emily
author list: Agent
  family name: Chebli
  given name: Gabriella
author list: Agent
  family name: Garfield
  given name: Claire
author list: Agent
  family name: Kubanek
  given name: Julia
author list: Agent
  family name: Stewart
  given name: Frank J.
doi: 10.7717/peerj.9493
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: ©2020 Patin et al.
attribution name: Patin et al.

Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam
type: item
type: AcademicArticle
description: Background Neisseria meningitidis remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged N. meningitidis isolates from these units and other units in proximity. Methods Strains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global N. meningitidis collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test. Results Genome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero®or Trumenba®, and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel s…
format: application/pdf
format: text/html
creator: Trang Thu Le
creator: Thach Xuan Tran
creator: Long Phi Trieu
creator: Christopher M. Austin
creator: Huong Minh Nguyen
creator: Dong Van Quyen
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.9502
publisher: PeerJ Inc.
rights: © 2020 Le et al.
abstract: Background Neisseria meningitidis remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged N. meningitidis isolates from these units and other units in proximity. Methods Strains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global N. meningitidis collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test. Results Genome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero®or Trumenba®, and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel s…
bibliographic citation: Le et al. (2020) Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam. PeerJ 8:e9502 https://doi.org/10.7717/peerj.9502
date submitted: 2020-03-04
date accepted: 2020-06-17
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Le
  given name: Trang Thu
author list: Agent
  family name: Tran
  given name: Thach Xuan
author list: Agent
  family name: Trieu
  given name: Long Phi
author list: Agent
  family name: Austin
  given name: Christopher M.
author list: Agent
  family name: Nguyen
  given name: Huong Minh
author list: Agent
  family name: Quyen
  given name: Dong Van
doi: 10.7717/peerj.9502
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: ©2020 Le et al.
attribution name: Le et al.

Habitat preferences rather than morphological traits affect the recovery process of Collembola (Arthropoda, Hexapoda) on a bare saline–alkaline land
type: item
type: AcademicArticle
description: The Songnen Plain of China was once an important grassland used for sheep grazing, but it has largely been degraded to bare saline-alkaline land (BSAL). BSAL consists of plant-free areas characterized by high soil pH values (up to 10) and salt and alkali (e.g., Na+ and Ca2+) contents, as well as low soil organic matter and water contents; thus, very few soil faunal species can survive on BSAL. The recovery of degraded ecosystems provides a great opportunity to investigate the reconstruction of belowground soil faunal communities. Collembola are a class of widespread and abundant soil fauna that can colonize this harsh environment. Habitat changes on BSAL promote aboveground revegetation, which greatly facilitates the recovery of Collembola. A soil transfer experiment on the BSAL of the Songnen Plain was conducted to study the effects of habitat and Collembola morphological traits on the recovery process of Collembola. Defaunated and with-fauna soil blocks were transferred among three habitats: BSAL, reclaimed arable land, and naturally revegetated grassland. The recovered Collembola in the transferred soil blocks were compared two, seven, and 12 weeks after the start of the experiment. The results showed that (1) the majority of the Collembola, regardless of their morphological traits, recovered in the defaunated soil blocks within 2 weeks; (2) generalists and habitat-preferring species recovered faster than specialists; (3) the average total abundance, species richness, and community composition of Collembola recovered to the natural levels in 2 weeks; and (4) 12 weeks after replacement, the highest average total abundance and species richness of Collembola were found in the arable land. Our results indicate that the majority of Collembola in this study, regardless of their dispersal type, which is related to their morphological traits, are fast dispersers, and their recovery speeds are mainly affected by habitat preferences. We suggest that the reclamation of BSAL…
format: application/pdf
format: text/html
creator: Zhen Ni
creator: Xiumin Yan
creator: Liang Chang
creator: Xin Sun
creator: Donghui Wu
creator: Bing Zhang
subject: Biodiversity
subject: Ecology
subject: Soil Science
description: doi:10.7717/peerj.9519
publisher: PeerJ Inc.
rights: © 2020 Ni et al.
abstract: The Songnen Plain of China was once an important grassland used for sheep grazing, but it has largely been degraded to bare saline-alkaline land (BSAL). BSAL consists of plant-free areas characterized by high soil pH values (up to 10) and salt and alkali (e.g., Na+ and Ca2+) contents, as well as low soil organic matter and water contents; thus, very few soil faunal species can survive on BSAL. The recovery of degraded ecosystems provides a great opportunity to investigate the reconstruction of belowground soil faunal communities. Collembola are a class of widespread and abundant soil fauna that can colonize this harsh environment. Habitat changes on BSAL promote aboveground revegetation, which greatly facilitates the recovery of Collembola. A soil transfer experiment on the BSAL of the Songnen Plain was conducted to study the effects of habitat and Collembola morphological traits on the recovery process of Collembola. Defaunated and with-fauna soil blocks were transferred among three habitats: BSAL, reclaimed arable land, and naturally revegetated grassland. The recovered Collembola in the transferred soil blocks were compared two, seven, and 12 weeks after the start of the experiment. The results showed that (1) the majority of the Collembola, regardless of their morphological traits, recovered in the defaunated soil blocks within 2 weeks; (2) generalists and habitat-preferring species recovered faster than specialists; (3) the average total abundance, species richness, and community composition of Collembola recovered to the natural levels in 2 weeks; and (4) 12 weeks after replacement, the highest average total abundance and species richness of Collembola were found in the arable land. Our results indicate that the majority of Collembola in this study, regardless of their dispersal type, which is related to their morphological traits, are fast dispersers, and their recovery speeds are mainly affected by habitat preferences. We suggest that the reclamation of BSAL…
bibliographic citation: Ni et al. (2020) Habitat preferences rather than morphological traits affect the recovery process of Collembola (Arthropoda, Hexapoda) on a bare saline–alkaline land. PeerJ 8:e9519 https://doi.org/10.7717/peerj.9519
date submitted: 2019-10-18
date accepted: 2020-06-19
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ni
  given name: Zhen
author list: Agent
  family name: Yan
  given name: Xiumin
author list: Agent
  family name: Chang
  given name: Liang
author list: Agent
  family name: Sun
  given name: Xin
author list: Agent
  family name: Wu
  given name: Donghui
author list: Agent
  family name: Zhang
  given name: Bing
doi: 10.7717/peerj.9519
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: © 2020 Ni et al.
attribution name: Ni et al.

Quantifying uncertainty in annual runoff due to missing data
type: item
type: AcademicArticle
description: Long-term streamflow datasets inevitably include gaps, which must be filled to allow estimates of runoff and ultimately catchment water budgets. Uncertainty introduced by filling gaps in discharge records is rarely, if ever, reported. We characterized the uncertainty due to streamflow gaps in a reference watershed at the Hubbard Brook Experimental Forest (HBEF) from 1996 to 2009 by simulating artificial gaps of varying duration and flow rate, with the objective of quantifying their contribution to uncertainty in annual streamflow. Gaps were filled using an ensemble of regressions relating discharge from nearby streams, and the predicted flow was compared to the actual flow. Differences between the predicted and actual runoff increased with both gap length and flow rate, averaging 2.8% of the runoff during the gap. At the HBEF, the sum of gaps averaged 22 days per year, with the lowest and highest annual uncertainties due to gaps ranging from 1.5 mm (95% confidence interval surrounding mean runoff) to 21.1 mm. As a percentage of annual runoff, uncertainty due to gap filling ranged from 0.2–2.1%, depending on the year. Uncertainty in annual runoff due to gaps was small at the HBEF, where infilling models are based on multiple similar catchments in close proximity to the catchment of interest. The method demonstrated here can be used to quantify uncertainty due to gaps in any long-term streamflow data set, regardless of the gap-filling model applied.
format: application/pdf
format: text/html
creator: Craig R. See
creator: Mark B. Green
creator: Ruth D. Yanai
creator: Amey S. Bailey
creator: John L. Campbell
creator: Jeremy Hayward
subject: Ecosystem Science
subject: Ecohydrology
description: doi:10.7717/peerj.9531
publisher: PeerJ Inc.
rights: ©
abstract: Long-term streamflow datasets inevitably include gaps, which must be filled to allow estimates of runoff and ultimately catchment water budgets. Uncertainty introduced by filling gaps in discharge records is rarely, if ever, reported. We characterized the uncertainty due to streamflow gaps in a reference watershed at the Hubbard Brook Experimental Forest (HBEF) from 1996 to 2009 by simulating artificial gaps of varying duration and flow rate, with the objective of quantifying their contribution to uncertainty in annual streamflow. Gaps were filled using an ensemble of regressions relating discharge from nearby streams, and the predicted flow was compared to the actual flow. Differences between the predicted and actual runoff increased with both gap length and flow rate, averaging 2.8% of the runoff during the gap. At the HBEF, the sum of gaps averaged 22 days per year, with the lowest and highest annual uncertainties due to gaps ranging from 1.5 mm (95% confidence interval surrounding mean runoff) to 21.1 mm. As a percentage of annual runoff, uncertainty due to gap filling ranged from 0.2–2.1%, depending on the year. Uncertainty in annual runoff due to gaps was small at the HBEF, where infilling models are based on multiple similar catchments in close proximity to the catchment of interest. The method demonstrated here can be used to quantify uncertainty due to gaps in any long-term streamflow data set, regardless of the gap-filling model applied.
bibliographic citation: See et al. (2020) Quantifying uncertainty in annual runoff due to missing data. PeerJ 8:e9531 https://doi.org/10.7717/peerj.9531
date submitted: 2020-04-21
date accepted: 2020-06-22
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: See
  given name: Craig R.
author list: Agent
  family name: Green
  given name: Mark B.
author list: Agent
  family name: Yanai
  given name: Ruth D.
author list: Agent
  family name: Bailey
  given name: Amey S.
author list: Agent
  family name: Campbell
  given name: John L.
author list: Agent
  family name: Hayward
  given name: Jeremy
doi: 10.7717/peerj.9531
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21

The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes
type: item
type: AcademicArticle
description: The development of explanatory models of protein sequence evolution has broad implications for our understanding of cellular biology, population history, and disease etiology. Here we analyze the GTEx transcriptome resource to quantify the effect of the transcriptome on protein sequence evolution in a multi-tissue framework. We find substantial variation among the central nervous system tissues in the effect of expression variance on evolutionary rate, with highly variable genes in the cortex showing significantly greater purifying selection than highly variable genes in subcortical regions (Mann–Whitney U p = 1.4 × 10−4). The remaining tissues cluster in observed expression correlation with evolutionary rate, enabling evolutionary analysis of genes in diverse physiological systems, including digestive, reproductive, and immune systems. Importantly, the tissue in which a gene attains its maximum expression variance significantly varies (p = 5.55 × 10−284) with evolutionary rate, suggesting a tissue-anchored model of protein sequence evolution. Using a large-scale reference resource, we show that the tissue-anchored model provides a transcriptome-based approach to predicting the primary affected tissue of developmental disorders. Using gradient boosted regression trees to model evolutionary rate under a range of model parameters, selected features explain up to 62% of the variation in evolutionary rate and provide additional support for the tissue model. Finally, we investigate several methodological implications, including the importance of evolutionary-rate-aware gene expression imputation models using genetic data for improved search for disease-associated genes in transcriptome-wide association studies. Collectively, this study presents a comprehensive transcriptome-based analysis of a range of factors that may constrain molecular evolution and proposes a novel framework for the study of gene function and disease mechanism.
format: application/pdf
format: text/html
creator: Patrick Evans
creator: Nancy J. Cox
creator: Eric R. Gamazon
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.9554
publisher: PeerJ Inc.
rights: © 2020 Evans et al.
abstract: The development of explanatory models of protein sequence evolution has broad implications for our understanding of cellular biology, population history, and disease etiology. Here we analyze the GTEx transcriptome resource to quantify the effect of the transcriptome on protein sequence evolution in a multi-tissue framework. We find substantial variation among the central nervous system tissues in the effect of expression variance on evolutionary rate, with highly variable genes in the cortex showing significantly greater purifying selection than highly variable genes in subcortical regions (Mann–Whitney U p = 1.4 × 10−4). The remaining tissues cluster in observed expression correlation with evolutionary rate, enabling evolutionary analysis of genes in diverse physiological systems, including digestive, reproductive, and immune systems. Importantly, the tissue in which a gene attains its maximum expression variance significantly varies (p = 5.55 × 10−284) with evolutionary rate, suggesting a tissue-anchored model of protein sequence evolution. Using a large-scale reference resource, we show that the tissue-anchored model provides a transcriptome-based approach to predicting the primary affected tissue of developmental disorders. Using gradient boosted regression trees to model evolutionary rate under a range of model parameters, selected features explain up to 62% of the variation in evolutionary rate and provide additional support for the tissue model. Finally, we investigate several methodological implications, including the importance of evolutionary-rate-aware gene expression imputation models using genetic data for improved search for disease-associated genes in transcriptome-wide association studies. Collectively, this study presents a comprehensive transcriptome-based analysis of a range of factors that may constrain molecular evolution and proposes a novel framework for the study of gene function and disease mechanism.
bibliographic citation: Evans et al. (2020) The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes. PeerJ 8:e9554 https://doi.org/10.7717/peerj.9554
date submitted: 2020-03-16
date accepted: 2020-06-24
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Evans
  given name: Patrick
author list: Agent
  family name: Cox
  given name: Nancy J.
author list: Agent
  family name: Gamazon
  given name: Eric R.
doi: 10.7717/peerj.9554
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: ©2020 Evans et al.
attribution name: Evans et al.

Ethyl pyruvate inhibits glioblastoma cells migration and invasion through modulation of NF-κB and ERK-mediated EMT
type: item
type: AcademicArticle
description: Background Glioblastoma is a grade IV glioma with the highest degree of malignancy and extremely high incidence. Because of the poor therapeutic effect of surgery and radiochemotherapy, glioblastoma has a high recurrence rate and lethality, and is one of the most challenging tumors in the field of oncology. Ethyl pyruvate (EP), a stable lipophilic pyruvic acid derivative, has anti-inflammatory, antioxidant, immunomodulatory and other cellular protective effects. It has been reported that EP has potent anti-tumor effects on many types of tumors, including pancreatic cancer, prostate cancer, liver cancer, gastric cancer. However, whether EP has anti-tumor effect on glioblastoma or not is still unclear. Methods Glioblastoma U87 and U251 cells were treated with different concentrations of EP for 24 h or 48 h. CCK8 assay and Colony-Formation assay were performed to test the viability and proliferation. Wound-healing assay and Transwell assay were carried out to measure cell invasion and migration. Western blot was not only used to detect the protein expression of epithelial-mesenchymal transition (EMT)-related molecules, but also to detect the expression and activation levels of NF-κB (p65) and Extracellular Signal Regulated Kinase (ERK). Results In glioblastoma U87 and U251 cells treated with EP, the viability, proliferation, migration, invasion abilities were inhibited in a dose-dependent manner. EP inhibited EMT and the activation of NF-κB (p65) and ERK. With NF-κB (p65) and ERK activated, EMT, migration and invasion of U87 and U251 cells were promoted. However the activation of NF-κB (p65) and ERK were decreased, EMT, migration and invasion abilities were inhibited in U87 and U251 cells treated with EP. Conclusion EP inhibits glioblastoma cells migration and invasion by blocking NF-κB and ERK-mediated EMT.
format: application/pdf
format: text/html
creator: Qing Huang
creator: Yongming Fu
creator: Shan Zhang
creator: Youxiang Zhang
creator: Simin Chen
creator: Zuping Zhang
subject: Cell Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.9559
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Background Glioblastoma is a grade IV glioma with the highest degree of malignancy and extremely high incidence. Because of the poor therapeutic effect of surgery and radiochemotherapy, glioblastoma has a high recurrence rate and lethality, and is one of the most challenging tumors in the field of oncology. Ethyl pyruvate (EP), a stable lipophilic pyruvic acid derivative, has anti-inflammatory, antioxidant, immunomodulatory and other cellular protective effects. It has been reported that EP has potent anti-tumor effects on many types of tumors, including pancreatic cancer, prostate cancer, liver cancer, gastric cancer. However, whether EP has anti-tumor effect on glioblastoma or not is still unclear. Methods Glioblastoma U87 and U251 cells were treated with different concentrations of EP for 24 h or 48 h. CCK8 assay and Colony-Formation assay were performed to test the viability and proliferation. Wound-healing assay and Transwell assay were carried out to measure cell invasion and migration. Western blot was not only used to detect the protein expression of epithelial-mesenchymal transition (EMT)-related molecules, but also to detect the expression and activation levels of NF-κB (p65) and Extracellular Signal Regulated Kinase (ERK). Results In glioblastoma U87 and U251 cells treated with EP, the viability, proliferation, migration, invasion abilities were inhibited in a dose-dependent manner. EP inhibited EMT and the activation of NF-κB (p65) and ERK. With NF-κB (p65) and ERK activated, EMT, migration and invasion of U87 and U251 cells were promoted. However the activation of NF-κB (p65) and ERK were decreased, EMT, migration and invasion abilities were inhibited in U87 and U251 cells treated with EP. Conclusion EP inhibits glioblastoma cells migration and invasion by blocking NF-κB and ERK-mediated EMT.
bibliographic citation: Huang et al. (2020) Ethyl pyruvate inhibits glioblastoma cells migration and invasion through modulation of NF-κB and ERK-mediated EMT. PeerJ 8:e9559 https://doi.org/10.7717/peerj.9559
date submitted: 2020-01-13
date accepted: 2020-06-25
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Qing
author list: Agent
  family name: Fu
  given name: Yongming
author list: Agent
  family name: Zhang
  given name: Shan
author list: Agent
  family name: Zhang
  given name: Youxiang
author list: Agent
  family name: Chen
  given name: Simin
author list: Agent
  family name: Zhang
  given name: Zuping
doi: 10.7717/peerj.9559
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: © 2020 Huang et al.
attribution name: Huang et al.

Prediction of human fetal–maternal blood concentration ratio of chemicals
type: item
type: AcademicArticle
description: Background The measurement of human fetal-maternal blood concentration ratio (logFM) of chemicals is critical for the risk assessment of chemical-induced developmental toxicity. While a few in vitro and ex vivo experimental methods were developed for predicting logFM of chemicals, the obtained experimental results are not able to directly predict in vivo outcomes. Methods A total of 55 chemicals with logFM values representing in vivo fetal-maternal blood ratio were divided into training and test datasets. An interpretable linear regression model was developed along with feature selection methods. Cross-validation on training dataset and prediction on independent test dataset were conducted to validate the prediction model. Results This study presents the first valid quantitative structure-activity relationship model following the Organisation for Economic Co-operation and Development (OECD) guidelines based on multiple linear regression for predicting in vivo logFM values. The autocorrelation descriptor AATSC1c and information content descriptor ZMIC1 were identified as informative features for predicting logFM. After the adjustment of the applicability domain, the developed model performs well with correlation coefficients of 0.875, 0.850 and 0.847 for model fitting, leave-one-out cross-validation and independent test, respectively. The model is expected to be useful for assessing human transplacental exposure.
format: application/pdf
format: text/html
creator: Chia-Chi Wang
creator: Pinpin Lin
creator: Che-Yu Chou
creator: Shan-Shan Wang
creator: Chun-Wei Tung
subject: Bioinformatics
subject: Toxicology
subject: Gynecology and Obstetrics
subject: Pharmacology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9562
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The measurement of human fetal-maternal blood concentration ratio (logFM) of chemicals is critical for the risk assessment of chemical-induced developmental toxicity. While a few in vitro and ex vivo experimental methods were developed for predicting logFM of chemicals, the obtained experimental results are not able to directly predict in vivo outcomes. Methods A total of 55 chemicals with logFM values representing in vivo fetal-maternal blood ratio were divided into training and test datasets. An interpretable linear regression model was developed along with feature selection methods. Cross-validation on training dataset and prediction on independent test dataset were conducted to validate the prediction model. Results This study presents the first valid quantitative structure-activity relationship model following the Organisation for Economic Co-operation and Development (OECD) guidelines based on multiple linear regression for predicting in vivo logFM values. The autocorrelation descriptor AATSC1c and information content descriptor ZMIC1 were identified as informative features for predicting logFM. After the adjustment of the applicability domain, the developed model performs well with correlation coefficients of 0.875, 0.850 and 0.847 for model fitting, leave-one-out cross-validation and independent test, respectively. The model is expected to be useful for assessing human transplacental exposure.
bibliographic citation: Wang et al. (2020) Prediction of human fetal–maternal blood concentration ratio of chemicals. PeerJ 8:e9562 https://doi.org/10.7717/peerj.9562
date submitted: 2020-04-20
date accepted: 2020-06-26
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chia-Chi
author list: Agent
  family name: Lin
  given name: Pinpin
author list: Agent
  family name: Chou
  given name: Che-Yu
author list: Agent
  family name: Wang
  given name: Shan-Shan
author list: Agent
  family name: Tung
  given name: Chun-Wei
doi: 10.7717/peerj.9562
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: ©2020 Wang et al.
attribution name: Wang et al.

The effects of “Fangcang, Huoshenshan, and Leishenshan” hospitals and environmental factors on the mortality of COVID-19
type: item
type: AcademicArticle
description: Background In December 2019, a novel coronavirus disease (COVID-19) broke out in Wuhan, China; however, the factors affecting the mortality of COVID-19 remain unclear. Methods Thirty-two days of data (the growth rate/mortality of COVID-19 cases) that were shared by Chinese National Health Commission and Chinese Weather Net were collected by two authors independently. Student’s t-test or Mann-Whitney U test was used to test the difference in the mortality of confirmed/severe cases before and after the use of “Fangcang, Huoshenshan, and Leishenshan” makeshift hospitals (MSHs). We also studied whether the above outcomes of COVID-19 cases were related to air temperature (AT), relative humidity (RH), or air quality index (AQI) by performing Pearson’s analysis or Spearman’s analysis. Results Eight days after the use of MSHs, the mortality of confirmed cases was significantly decreased both in Wuhan (t = 4.5, P < 0.001) and Hubei (U = 0, P < 0.001), (t and U are the test statistic used to test the significance of the difference). In contrast, the mortality of confirmed cases remained unchanged in non-Hubei regions (U = 76, P = 0.106). While on day 12 and day 16 after the use of MSHs, the reduce in mortality was still significant both in Wuhan and Hubei; but in non-Hubei regions, the reduce also became significant this time (U = 123, P = 0.036; U = 171, P = 0.015, respectively). Mortality of confirmed cases was found to be negatively correlated with AT both in Wuhan (r = − 0.441, P = 0.012) and Hubei (r = − 0.440, P = 0.012). Also, both the growth rate and the mortality of COVID-19 cases were found to be significantly correlated with AQI in Wuhan and Hubei. However, no significant correlation between RH and the growth rate/mortality of COVID-19 cases was found in our study. Conclusions Our findings indicated that both the use of MSHs, the rise of AT, and the improvement of air quality were beneficial to the survival of COVID-19 patients.
format: application/pdf
format: text/html
creator: Yuwen Cai
creator: Tianlun Huang
creator: Xin Liu
creator: Gaosi Xu
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.9578
publisher: PeerJ Inc.
rights: © 2020 Cai et al.
abstract: Background In December 2019, a novel coronavirus disease (COVID-19) broke out in Wuhan, China; however, the factors affecting the mortality of COVID-19 remain unclear. Methods Thirty-two days of data (the growth rate/mortality of COVID-19 cases) that were shared by Chinese National Health Commission and Chinese Weather Net were collected by two authors independently. Student’s t-test or Mann-Whitney U test was used to test the difference in the mortality of confirmed/severe cases before and after the use of “Fangcang, Huoshenshan, and Leishenshan” makeshift hospitals (MSHs). We also studied whether the above outcomes of COVID-19 cases were related to air temperature (AT), relative humidity (RH), or air quality index (AQI) by performing Pearson’s analysis or Spearman’s analysis. Results Eight days after the use of MSHs, the mortality of confirmed cases was significantly decreased both in Wuhan (t = 4.5, P < 0.001) and Hubei (U = 0, P < 0.001), (t and U are the test statistic used to test the significance of the difference). In contrast, the mortality of confirmed cases remained unchanged in non-Hubei regions (U = 76, P = 0.106). While on day 12 and day 16 after the use of MSHs, the reduce in mortality was still significant both in Wuhan and Hubei; but in non-Hubei regions, the reduce also became significant this time (U = 123, P = 0.036; U = 171, P = 0.015, respectively). Mortality of confirmed cases was found to be negatively correlated with AT both in Wuhan (r = − 0.441, P = 0.012) and Hubei (r = − 0.440, P = 0.012). Also, both the growth rate and the mortality of COVID-19 cases were found to be significantly correlated with AQI in Wuhan and Hubei. However, no significant correlation between RH and the growth rate/mortality of COVID-19 cases was found in our study. Conclusions Our findings indicated that both the use of MSHs, the rise of AT, and the improvement of air quality were beneficial to the survival of COVID-19 patients.
bibliographic citation: Cai et al. (2020) The effects of “Fangcang, Huoshenshan, and Leishenshan” hospitals and environmental factors on the mortality of COVID-19. PeerJ 8:e9578 https://doi.org/10.7717/peerj.9578
date submitted: 2020-04-18
date accepted: 2020-06-30
issued: 2020-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Yuwen
author list: Agent
  family name: Huang
  given name: Tianlun
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Xu
  given name: Gaosi
doi: 10.7717/peerj.9578
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-21
copyright: ©2020 Cai et al.
attribution name: Cai et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359